Linking NDVI and leaf senescence in high arctic tundra plants: Soil moisture control on senescence phenology revealed by direct observations and NDVI sensors
Data files
Sep 11, 2026 version files 1.58 MB
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climate_data.csv
714 B
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data_analysis_main_revised_v3.Rmd
45.72 KB
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ndvi_2023.csv
1.38 MB
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README.md
8.32 KB
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senescence_datatable.csv
134.36 KB
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trs_dates_species_level.csv
4.79 KB
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trs_dates_weighted_50.csv
684 B
Abstract
Senescence phenology in Tundra plants is an understudied topic in plant ecology, limiting our understanding of trophic processes and vegetation-climate feedbacks linked to the autumn season in Arctic regions. In-situ Normalized Difference Vegetation Index (NDVI) sensors deployed at plot-level hold the potential to increase availability of quality data on senescence phenology by avoiding problems common to satellite-based remote sensing and intensive field campaigns in remote sites. We evaluated the relationship between plot-level NDVI and the progression of species level leaf senescence, as well as the suitability of NDVI midpoints as a metric to monitor community-wide senescence timing in tundra communities in high Arctic Svalbard. Ground validation data consisted of weekly observation of senesced leaf area (%) of 275 tagged plant individuals belonging to 11 species in six plant communities throughout the autumn 2023. Furthermore, we analyzed the influence of microclimate (soil moisture, soil temperature, and snowmelt date) on the timing cross-species senescence thresholds (25, 50, and 75 % senesced leaf area). Finally, we tested whether this analysis could be replicated using NDVI midpoints instead of field observations. We found that senescence progression was associated with a linear decrease in NDVI but the strength of the association varied between plant communities. NDVI midpoints occurred when community-weighted senescence had reached about 50 % (49 %, CI: [33 % - 69 %]) on average across all communities, making the NDVI midpoint a suitable metric for deriving meaningful end-of-season dates. NDVI midpoint occurred within 0-4 days of date when community-weighted senescence reached 50 %, excepts in graminoid-rich wetlands where the NDVI midpoint occurred about 12 days later. Out of the tested microclimatic parameters, soil moisture was the most important one. Here, all phenostages occurred later in wetter sites compared to drier sites. Furthermore, 25 % senescence occurred earlier in warmer sites. Date of NDVI midpoint similarly occurred later in wetter sites compared to dry sites. Using NDVI midpoints thus replicated the results based on field-derived phenostages. We conclude that plot-level NDVI midpoints are a promising metric for monitoring senescence phenology in tundra plants, with the potential to be used in future studies for investigating environmental drivers of senescence.
Dataset DOI: 10.5061/dryad.6m905qgf1
Description of the data and file structure
Daily in-situ Normalized Difference Vegetation Index (NDVI) data was collected at plot level (n = 20) in six common plant communities in high Arctic Svalbard from June - September 2023. A ground validation effort to validate the use of NDVI for monitoring senescence phenology in Arctic tundra plants was carried out throughout the autumn period where senescence occurred (late-July to late-September). Ground validation data consisted of weekly observations of senescence progression of 275 tagged plant individuals, representing the dominant species in each plant community. Here, 11 species were monitored in total. In addition, soil moisture and soil temperatures were logged in each plot from June-September while spring snowmelt date was derived from Sentinel-2 NDSI.
Files and variables
File: climate_data.csv
Description: A file containing microclimatic variables at plot level used for the analyses on microclimatic impacts on senescence timing using field observations of tagged plants and NDVI midpoints.
Variables
- plot_ID: Variable containing plot IDs. The first three letters of each ID indicate plant community type.
- snowmelt: Spring snowmelt dates dereived from Sentinel-2 NDSI.
- TDD: Soil thawing degree days (cumulative temperature sum for days with mean temperature above 0 degree Celcius) from 11 June - 15 July, recorded at 10 cm depth. 'NA' (not available) values indicate missing data points due to malfunction of data loggers in four plots.
- moisture: Average soil moisture recorded at 10 cm depth between 11 June - 11 August. 'NA' (not available) values indicate missing data points due to malfunction of data loggers in four plots.
File: trs_dates_species_level.csv
Description: File containing the dates (DOY) where senesced leaf area (%) crossed the three thresholds: 25 %, 50 %, and 75 % for each tagged plant individual. These dates were derived from interpolation between weekly observations using logistic regression models.
Variables
- plot_ID: Variable containing plot IDs.
- sp: Abbreviated plant species names
- sp_latin: Full plant species names
- community: Plant community type
- doy_at_025: Model estimate of the DOY when a plant individual reached 25 % green leaf area (=75 % senesced leaf area). 'NA' (not applicable) values represent missing data points where senesced leaf area (%) did not cross the 25 % threshold.
- doy_at_050: Model estimate of the DOY when a plant individual reached 50% green leaf area (=50% senesced leaf area). 'NA' (not applicable) values represent missing data points where senesced leaf area (%) did not cross the 50 % threshold.
- doy_at_075: Model estimate of the DOY when a plant individual reached 75 % green leaf area (=25 % senesced leaf area). 'NA' (not applicable) values represent missing data points where senesced leaf area (%) did not cross the 75 % threshold.
- se_at_025: Standard errors associated with doy_at_025 estimates. 'NA' (not applicable) values represent missing data points in cases where doy_at_025 is 'NA'.
- se_at_050: Standard errors associated with doy_at_050 estimates. 'NA' (not applicable) values represent missing data points in cases where doy_at_050 is 'NA'.
- se_at_075: Standard errors associated with doy_at_075 estimates. 'NA' (not applicable) values represent missing data points in cases where doy_at_075 is 'NA'.
File: ndvi_2023.csv
Description: NDVI recorded every four hours from June - September at plot level from two meters height.
Variables
- DateTime: Timestamp indicating date and time for each recording.
- rack_id: ID of the NDVI mast and its associated vegetation plot. Synonymous with 'plot_ID'.
- hemispherical_NIR: Near-infrared reflectance recorded from hemispherical sensor. Used for correction of hemispherical effects on vegetation NDVI. 'NA' (not available) values represent missing data points in a few cases where sensors failed to record a valid irradiance value.
- hemispherical_red: Red reflectance recorded from hemispherical sensor. Used for correction of hemispherical effects on vegetation NDVI. 'NA' (not available) values represent missing data points in a few cases where sensors failed to record a valid irradiance value.
- reflected_NIR: Near-infrared reflectance from vegetation.
- reflected_red: Red reflectance from vegetation.
- NDVI_uncorrected: Regular NDVI calculated by NDVI = (reflected_NIR - reflected_red) / (reflected_NIR + reflected_red). 'NA' (not available) values represent missing data points in a nine cases where division by a near-zero value caused the computation to fail.
- NDVI_corrected: Hemispherically corrected NDVI calculated by NDVI = ((reflected_NIR/hemispherical_NIR) - (reflected_red/hemispherical_red)) / ((reflected_NIR/hemispherical_NIR) + (reflected_red/hemispherical_red)). 'NA' (not available) values represent missing data points primarily at night time between 00:00 - 04:00 AM where recorded hemispherical irradiance (hemispherical_red and hemispherical_NIR) were very low and resulted in computation errors when dividing by near-zero values.
File: senescence_datatable.csv
Description: File containing weekly observation of the progression of senescence recorded as percent senesced leaf area out of the total live leaf area for each tagged plant individual.
Variables
- date: Date for each observation.
- doy: Date in yearday (DOY)
- community: Plant community type
- plot_ID: Variable containing plot IDs.
- plant_ID: Variable containing plant IDs for each tagged plant.
- sp: Abbreviated plant species name.
- sp_latin: Full plant species name.
- i_sen_perc: Recorded senesced leaf area (%) out of total live leaf area for each plant individual on each observation date. 'NA' (not available) values represent missing data points in cases where the field team failed to locate a given plant_ID and/or record i_sen_perc.
- i_green_perc: Recorded green leaf area (%) out of total live leaf area for each plant individual on each observation date. 'NA' (not available) values represent missing data points in cases where the field team failed to locate a given plant_ID and/or record i_green_perc.
File: trs_dates_weighted_50.csv
Description: File containing the dates (DOY) where community-weighted senesced leaf area ('CS'; %) crossed 50 % for each vegetation plot. Here, each species' contribution to the community-weighted mean is weighted by its percent ground cover (%) relative to the other dominant plant species. These dates were derived from interpolation between weekly observations using logistic regression models.
Variables
- plot_ID: Variable containing plot IDs.
- weighted50: Model estimate of the date (DOY) where community-weighted senesced leaf area (CS; %) crossed 50 % (CS50 %) in each plot. 'NA' (not applicable) values represent missing data points where CS did not cross the 50 % threshold.
- se_at_050: Standard errors associated with the 'weighted50' estimate. 'NA' (not applicable) values represent missing data points in cases where weighted50 is 'NA'.
- type: Plant community type.
File: data_analysis_main_revised_v3.Rmd
Description: An R markdown file containing all the code necessary to replicate statistical results and figures for the paper.
Code/software
All data files are in .csv format and can be viewed using your favorite text editor (notepad++ recommended).
The R script 'data_analysis_main.Rmd' included is an Rmarkdown and can be run in Rstudio. The script contains the code necessary to reproduce all the results and figures shown in the paper.
Versions used to run the code successfully by the authors were: RStudio 2024.09.1+394 for windows with R version 4.4.1 (2024-06-14 ucrt). Installed packages required with versions used were:
Package Version
easystats 0.7.3
lme4 1.1.35.5
lmerTest 3.1.3
tidyverse 2.0.0
lubridate 1.9.3
stringi 1.8.4
zoo 1.8.12
scales 1.4.0
phenopix 2.4.4
cowplot 1.1.3
